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Method: Tree-based differential testing using inferential uncertainty for RNA-seq
- Noor Pratap Singh,
- Euphy Y. Wu,
- Jason Fan,
- Michael I. Love,
- and Rob Patro
Genome Res. October 2025 35: 2326-2338; Published in Advance August 21, 2025, doi:10.1101/gr.279981.124
...to uncertainty when trying to quantify transcript abundances. Uncertainty can also exist for gene abundance estimates when the reads belong to shared sequences within the genes (e.g., homologous genes); however, in general, gene-level estimates will be more precise compared to transcripts. One approach...
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Method: Seamless, rapid, and accurate analyses of outbreak genomic data using split k-mer analysis
- Romain Derelle,
- Johanna von Wachsmann,
- Tommi Mäklin,
- Joel Hellewell,
- Timothy Russell,
- Ajit Lalvani,
- Leonid Chindelevitch,
- Nicholas J. Croucher,
- Simon R. Harris,
- and John A. Lees
Genome Res. October 2024 34: 1661-1673; Published in Advance October 15, 2024, doi:10.1101/gr.279449.124
...with a different middle base, homology between the two middle bases can be hypothesized and their difference interpreted as a SNP. The data conversion into split k-mers essentially creates independent local references for each genomic position of the strains of interest on the fly, enabling alignment...
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Research: The genomic basis of evolutionary differentiation among honey bees
- Bertrand Fouks,
- Philipp Brand,
- Hung N. Nguyen,
- Jacob Herman,
- Francisco Camara,
- Daniel Ence,
- Darren E. Hagen,
- Katharina J. Hoff,
- Stefanie Nachweide,
- Lars Romoth,
- Kimberly K.O. Walden,
- Roderic Guigo,
- Mario Stanke,
- Giuseppe Narzisi,
- Mark Yandell,
- Hugh M. Robertson,
- Nikolaus Koeniger,
- Panuwan Chantawannakul,
- Michael C. Schatz,
- Kim C. Worley,
- Gene E. Robinson,
- Christine G. Elsik,
- and Olav Rueppell
Genome Res. July 2021 31: 1203-1215; Published in Advance May 4, 2021, doi:10.1101/gr.272310.120
...University, New York, New York 10065, USA; 5MU Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri 65211, USA; 6Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08036 Barcelona, Spain; 7School of Forest Resources and Conservation...
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Resource: Alignathon: a competitive assessment of whole-genome alignment methods
- Dent Earl,
- Ngan Nguyen,
- Glenn Hickey,
- Robert S. Harris,
- Stephen Fitzgerald,
- Kathryn Beal,
- Igor Seledtsov,
- Vladimir Molodtsov,
- Brian J. Raney,
- Hiram Clawson,
- Jaebum Kim,
- Carsten Kemena,
- Jia-Ming Chang,
- Ionas Erb,
- Alexander Poliakov,
- Minmei Hou,
- Javier Herrero,
- William James Kent,
- Victor Solovyev,
- Aaron E. Darling,
- Jian Ma,
- Cedric Notredame,
- Michael Brudno,
- Inna Dubchak,
- David Haussler,
- and Benedict Paten
Genome Res. December 2014 24: 2077-2089; Published in Advance October 1, 2014, doi:10.1101/gr.174920.114
...Alignathon: a competitive assessment of whole-genome alignment methods Dent Earl 1 , 2 , Ngan Nguyen 1 , 2 , Glenn Hickey 3 , Robert S. Harris 4 , Stephen Fitzgerald 5 , Kathryn Beal 5 , Igor Seledtsov 6...
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Method: GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly
- Daniel L. Cameron,
- Jan Schröder,
- Jocelyn Sietsma Penington,
- Hongdo Do,
- Ramyar Molania,
- Alexander Dobrovic,
- Terence P. Speed,
- and Anthony T. Papenfuss
Genome Res. December 2017 27: 2050-2060; Published in Advance November 2, 2017, doi:10.1101/gr.222109.117
...the repair. Microhomology at the breakpoints introduces uncertainty into the breakpoint position call, which is resolved if nontemplate sequence is also present. As a consequence of aligner behavior, unhandled sequence homology can result in two separate variant calls (one at each edge of the homology...
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Resource: Indels, structural variation, and recombination drive genomic diversity in Plasmodium falciparum
- Alistair Miles,
- Zamin Iqbal,
- Paul Vauterin,
- Richard Pearson,
- Susana Campino,
- Michel Theron,
- Kelda Gould,
- Daniel Mead,
- Eleanor Drury,
- John O'Brien,
- Valentin Ruano Rubio,
- Bronwyn MacInnis,
- Jonathan Mwangi,
- Upeka Samarakoon,
- Lisa Ranford-Cartwright,
- Michael Ferdig,
- Karen Hayton,
- Xin-zhuan Su,
- Thomas Wellems,
- Julian Rayner,
- Gil McVean,
- and Dominic Kwiatkowski
Genome Res. September 2016 26: 1288-1299; Published in Advance August 16, 2016, doi:10.1101/gr.203711.115
...for the given indel class (STR/non-STR). Deep sequencing of P. falciparum crosses Genome Research 1291 www..org (see also Fig. 1 in Youds and Boulton 2011). We inferred recombination events from the size and arrangement of parental haplotype blocks transmitted to the progeny (Methods; Supplemental Information...
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Methods: Græmlin: General and robust alignment of multiple large interaction networks
- Jason Flannick,
- Antal Novak,
- Balaji S. Srinivasan,
- Harley H. McAdams,
- and Serafim Batzoglou
Genome Res. September 2006 16: 1169-1181; Published in Advance August 9, 2006, doi:10.1101/gr.5235706
...complexes and metabolic pathways. To assess Græmlin's performance, we have developed the first quantitative benchmarks for network alignment, which allow comparisons of algorithms in terms of their ability to recapitulate the KEGG database of conserved functional modules. We find that Græmlin achieves...
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Methods: Inferring genomic flux in bacteria
- Xavier Didelot,
- Aaron Darling,
- and Daniel Falush
Genome Res. February 2009 19: 306-317; Published in Advance November 17, 2008, doi:10.1101/gr.082263.108
...studies of genomic flux have used annotated genes as the units of gain and loss. In the standard inference protocol, genes annotated in sequenced s are first assigned to orthologous groups on the basis of sequence homology. Paralogs in multicopy gene families are either disambiguated or discarded...
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Methods: Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs
- Benedict Paten,
- Javier Herrero,
- Kathryn Beal,
- Stephen Fitzgerald,
- and Ewan Birney
Genome Res. November 2008 18: 1814-1828; Published in Advance October 10, 2008, doi:10.1101/gr.076554.108
.... Abstract Pairwise whole-genome alignment involves the creation of a homology map, capable of performing a near complete transformation of one genome into another. For multiple genomes this problem is generalized to finding a set of consistent homology maps for converting each genome in the set of aligned...
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METHODS: LineUp: Statistical Detection of Chromosomal Homology With Application to Plant Comparative Genomics
- Steve Hampson,
- Aoife McLysaght,
- Brandon Gaut,
- and Pierre Baldi
Genome Res. May 1, 2003 13: 999-1010; Published in Advance April 14, 2003, doi:10.1101/gr.814403
...the basis for studies of genome organization, comparative genomics, and evolutionary genomics. Identification of these regions can be based on either synteny or colinearity, but there are few methods to test statistically for significant evidence of homology. In the present study, we improve a preexisting...

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